Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.

Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.

Ordinal regression models for zero-inflated and/or over-dispersed count data.

Count data commonly arise in natural sciences but adequately modeling these data is challenging due to zero-inflation and over-dispersion. While multiple parametric modeling approaches have been proposed, unfortunately there is no consensus regarding how to choose the best model. In this article, we propose a ordinal regression model (MN) as a default model for count data given that this model is shown to fit well data that arise from several types of discrete distributions. We extend this model to allow for automatic model selection (MN-MS) and show that the MN-MS model generates superior inference when compared to using the full model or more traditional model selection approaches. The MN-MS model is used to determine how human biting rate of mosquitoes, known to be able to transmit malaria, are influenced by environmental factors in the Peruvian Amazon. The MN-MS model had one of the best fit and out-of-sample predictive skill amongst all models. While A. darlingi is strongly associated with highly anthropized landscapes, all the other mosquito species had higher mean biting rates in landscapes with a lower fraction of exposed soil and urban area, revealing a striking shift in species composition. We believe that the MN and MN-MS models are valuable additions to the modelling toolkit employed by environmental modelers and quantitative ecologists.